Even easier than Espript is ConSurf http://consurf.tau.ac.il/
You can either supply your own PDB or use one from RCSB. You can also supply your own alignment or let Consurf build one from a PSI-BLAST run. The server returns several outputs, including: *The alignment it used to generate the surface conservation (in case you had it build one automatically) *A nice list of each residue in your favorite protein, the relative conservation (scale of 1-10) of that position, and what other residues are found at that position in other organisms. This list is, frankly, incredibly handy. *PDB with the B-factor column replaced with relative conservation. If you open this PDB and run the color_b script (http://adelie.biochem.queensu.ca/~rlc/work/pymol/) with a two-color ramped gradient (eg - white->green) you'll have a very intuitive view of potential "hot spots". Enjoy! -- Jacob Corn UC Berkeley - Berger Lab Lab: 510-643-9491 Cell: 925-408-8579 jc...@uclink.berkeley.edu Friday, May 21, 2004, 8:28:45 AM, you wrote: cmlcau> Hello PyMol community! cmlcau> is there any way to display sequence conservation on the surface of a cmlcau> protein? cmlcau> i.e. to use the info I have in a sequence alignment. cmlcau> do I have to do this by hand? cmlcau> Thanks, cmlcau> Camille cmlcau> ------------------------------------------------------- cmlcau> This SF.Net email is sponsored by: Oracle 10g cmlcau> Get certified on the hottest thing ever to hit the market... Oracle 10g. cmlcau> Take an Oracle 10g class now, and we'll give you the exam FREE. cmlcau> http://ads.osdn.com/?ad_id=3149&alloc_id=8166&op=click cmlcau> _______________________________________________ cmlcau> PyMOL-users mailing list cmlcau> PyMOL-users@lists.sourceforge.net cmlcau> https://lists.sourceforge.net/lists/listinfo/pymol-users
